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Statistical Applications in Genetics and Molecular Biology

2002 - 2009

from Berkeley Electronic Press
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Volume 8, issue 1, 2009

Inferring Dynamic Genetic Networks with Low Order Independencies Downloads
Sophie Lèbre
Hypothesis Tests for Point-Mass Mixture Data with Application to `Omics Data with Many Zero Values Downloads
Sandra Taylor and Katherine Pollard
A Multiple Testing Approach to High-Dimensional Association Studies with an Application to the Detection of Associations between Risk Factors of Heart Disease and Genetic Polymorphisms Downloads
José A. Ferreira, Johannes Berkhof, Olga Souverein and Koos Zwinderman
Composite Likelihood Modeling of Neighboring Site Correlations of DNA Sequence Substitution Rates Downloads
Ling Deng and Dirk F. Moore
A Nonlinear Mixed-Effects Model for Estimating Calibration Intervals for Unknown Concentrations in Two-Color Microarray Data with Spike-Ins Downloads
Pushpike J. Thilakarathne, Geert Verbeke, Kristof Engelen and Kathleen Marchal
A Unified Mixed Effects Model for Gene Set Analysis of Time Course Microarray Experiments Downloads
Lily Wang, Xi Chen, Russell D. Wolfinger, Jeffrey L. Franklin, Robert J. Coffey and Bing Zhang
Statistical Screening Method for Genetic Factors Influencing Susceptibility to Common Diseases in a Two-Stage Genome-Wide Association Study Downloads
Yasunori Sato, Nan Laird, Hideki Suganami, Chikuma Hamada, Naoto Niki, Isao Yoshimura and Teruhiko Yoshida
A Regularized Regression Approach for Dissecting Genetic Conflicts that Increase Disease Risk in Pregnancy Downloads
Shaoyu Li, Qing Lu, Wenjiang Fu, Roberto Romero and Yuehua Cui
Transmission Disequilibrium Test Power and Sample Size in the Presence of Locus Heterogeneity Downloads
Chuanwen Chen, Guang Yang, Steven Buyske, Tara Matise, Stephen J. Finch and Derek Gordon
Characterizing the D2 Statistic: Word Matches in Biological Sequences Downloads
Sylvain Forêt, Susan R. Wilson and Conrad J. Burden
MC-Normalization: A Novel Method for Dye-Normalization of Two-Channel Microarray Data Downloads
Mattias Landfors, Jessica Fahlén and Patrik Rydén
M-quantile Regression Analysis of Temporal Gene Expression Data Downloads
Veronica Vinciotti and Keming Yu
Modeling Dependence in Methylation Patterns with Application to Ovarian Carcinomas Downloads
Michelle R. Lacey and Melanie Ehrlich
Dimension Reduction of Microarray Data in the Presence of a Censored Survival Response: A Simulation Study Downloads
Tuan S. Nguyen and Javier Rojo
Calculating Asymptotic Significance Levels of the Constrained Likelihood Ratio Test with Application to Multivariate Genetic Linkage Analysis Downloads
Nathan J. Morris, Robert Elston and Catherine M. Stein
A Statistical Model for Genetic Mapping of Viral Infection by Integrating Epidemiological Behavior Downloads
Yao Li, Arthur Berg, Myron N. Chang, Ping Du, Kwangmi Ahn, David Mauger, Duanping Liao and Rongling Wu
Identifying Individuals in a Complex Mixture of DNA with Unknown Ancestry Downloads
Joshua Sampson and Hongyu Zhao
Prediction of Motifs Based on a Repeated-Measures Model for Integrating Cross-Species Sequence and Expression Data Downloads
Elizabeth A. Siewert and Katerina J. Kechris
Ancestral Recombination Graphs under Non-Random Ascertainment, with Applications to Gene Mapping Downloads
Ola Hössjer, Linda Hartman and Keith Humphreys
Rotation Testing in Gene Set Enrichment Analysis for Small Direct Comparison Experiments Downloads
Guro Dørum, Lars Snipen, Margrete Solheim and Solve Sæbø
A Multivariate Growth Curve Model for Ranking Genes in Replicated Time Course Microarray Data Downloads
Jemila S. Hamid and Joseph Beyene
Estimation of Selection Intensity under Overdominance by Bayesian Methods Downloads
Erkan Ozge Buzbas, Paul Joyce and Zaid Abdo
Model Selection Based on FDR-Thresholding Optimizing the Area under the ROC-Curve Downloads
Alexandra C. Graf and Peter Bauer
Adaptive Transmission Disequilibrium Test for Family Trio Design Downloads
Min Yuan, Xin Tian, Gang Zheng and Yaning Yang
Sequential Analysis for Microarray Data Based on Sensitivity and Meta-Analysis Downloads
Guillemette Marot and Claus-Dieter Mayer
A Non-Homogeneous Hidden-State Model on First Order Differences for Automatic Detection of Nucleosome Positions Downloads
Pei Fen Kuan, Dana Huebert, Audrey Gasch and Sunduz Keles
Extensions of Sparse Canonical Correlation Analysis with Applications to Genomic Data Downloads
Daniela M. Witten and Robert J. Tibshirani
Bayesian Unsupervised Learning with Multiple Data Types Downloads
Phaedra Agius, Yiming Ying and Colin Campbell
A Parametric Model for Analyzing Anticipation in Genetically Predisposed Families Downloads
Klaus Larsen, Janne Petersen, Inge Bernstein and Mef Nilbert
Increase of Rejection Rate in Case-Control Studies with the Differential Genotyping Error Rates Downloads
Kwangmi Ahn, Derek Gordon and Stephen J. Finch
Incorporating Duplicate Genotype Data into Linear Trend Tests of Genetic Association: Methods and Cost-Effectiveness Downloads
Bryce Borchers, Marshall Brown, Brian McLellan, Airat Bekmetjev and Nathan L. Tintle
Weighted Multiple Hypothesis Testing Procedures Downloads
Guolian Kang, Keying Ye, Nianjun Liu, David B. Allison and Guimin Gao
Multilevel Comparison of Dendrograms: A New Method with an Application for Genetic Classifications Downloads
János Podani, Attila Engloner and Agnes Major
Univariate Shrinkage in the Cox Model for High Dimensional Data Downloads
Robert J. Tibshirani
Balanced Gradient Boosting from Imbalanced Data for Clinical Outcome Prediction Downloads
Reiji Teramoto
Orthology-Based Multilevel Modeling of Differentially Expressed Mouse and Human Gene Pairs Downloads
Benjamin A. Ogorek and Leonard A. Stefanski
Testing of Chromosomal Clumping of Gene Properties Downloads
Luciano Fernandez-Ricaud, Daniel Dalevi, Anders Blomberg and Olle Nerman
A Multilocus Model for Constructing a Linkage Disequilibrium Map in Human Populations Downloads
Qin Li and Rongling Wu
Impact of Population Stratification on Family-Based Association Tests with Longitudinal Measurements Downloads
Xiao Ding, Scott Weiss, Benjamin Raby, Christoph Lange and Nan M. Laird
Score Statistics for Mapping Quantitative Trait Loci Downloads
Myron N. Chang, Rongling Wu, Samuel S. Wu and George Casella
Two-Stage Model-Based Clustering for Liquid Chromatography Mass Spectrometry Data Analysis Downloads
Marta Łuksza, Bogusław Kluge, Jerzy Ostrowski, Jakub Karczmarski and Anna Gambin
Survival Analysis with High-Dimensional Covariates: An Application in Microarray Studies Downloads
David Engler and Yi Li
Detecting Outlier Samples in Microarray Data Downloads
Albert D. Shieh and Yeung Sam Hung
Modified FDR Controlling Procedure for Multi-Stage Analyses Downloads
Catherine Tuglus and Mark J. van der Laan
A Bayesian Analysis Strategy for Cross-Study Translation of Gene Expression Biomarkers Downloads
Joseph Lucas, Carlos Carvalho and Mike West
Normalization Method for Transcriptional Studies of Heterogeneous Samples – Simultaneous Array Normalization and Identification of Equivalent Expression Downloads
Li-Xuan Qin and Jaya M. Satagopan
Sparse Canonical Correlation Analysis with Application to Genomic Data Integration Downloads
Elena Parkhomenko, David Tritchler and Joseph Beyene

Volume 7, issue 2, 2008

Empirical Bayes Logistic Regression Downloads
Foteini Strimenopoulou and Philip J. Brown
A Classification Model for the Leiden Proteomics Competition Downloads
Huub C. J. Hoefsloot, Suzanne Smit and Age K. Smilde
Classification of Breast Cancer versus Normal Samples from Mass Spectrometry Profiles Using Linear Discriminant Analysis of Important Features Selected by Random Forest Downloads
Somnath Datta
Principal Component Discriminant Analysis Downloads
Tom Fearn
Developing a Discrimination Rule between Breast Cancer Patients and Controls Using Proteomics Mass Spectrometric Data: A Three-Step Approach Downloads
A. Geert Heidema and Nico Nagelkerke
Application of the Random Forest Classification Method to Peaks Detected from Mass Spectrometric Proteomic Profiles of Cancer Patients and Controls Downloads
Jennifer H. Barrett and David A. Cairns
Organizing a Competition on Clinical Mass Spectrometry Based Proteomic Diagnosis Downloads
Bart Mertens
Case-Control Breast Cancer Study of MALDI-TOF Proteomic Mass Spectrometry Data on Serum Samples Downloads
Martijn P. J. van der Werff, Bart Mertens, Mirre E. de Noo, Marco R. Bladergroen, Hans C. Dalebout, Rob A. E. M. Tollenaar and Andre M. Deelder
Breast Cancer Diagnosis from Proteomic Mass Spectrometry Data: A Comparative Evaluation Downloads
David J. Hand
Assessing the Validity Domains of Graphical Gaussian Models in Order to Infer Relationships among Components of Complex Biological Systems Downloads
Fanny Villers, Brigitte Schaeffer, Caroline Bertin and Sylvie Huet
Clinical Mass Spectrometry Proteomic Diagnosis by Conformal Predictors Downloads
Alex Gammerman, Ilia Nouretdinov, Brian Burford, Alexey Chervonenkis, Vladimir Vovk and Zhiyuan Luo
A Cross-Validation Study to Select a Classification Procedure for Clinical Diagnosis Based on Proteomic Mass Spectrometry Downloads
Dirk Valkenborg, Suzy Van Sanden, Dan Lin, Adetayo Kasim, Qi Zhu, Philippe Haldermans, Ivy Jansen, Ziv Shkedy and Tomasz Burzykowski
Support Vector Machine Approach to Separate Control and Breast Cancer Serum Samples Downloads
Thang V. Pham, Mark A. van de Wiel and Connie R. Jimenez
Autocorrelated Logistic Ridge Regression for Prediction Based on Proteomics Spectra Downloads
Jelle J. Goeman
International Competition on Mass Spectrometry Proteomic Diagnosis Downloads
Bart Mertens

Volume 7, issue 1, 2008

Structure Learning in Nested Effects Models Downloads
Achim Tresch and Florian Markowetz
Calculating Confidence Intervals for Prediction Error in Microarray Classification Using Resampling Downloads
Wenyu Jiang, Sudhir Varma and Richard Simon
Comparing the Characteristics of Gene Expression Profiles Derived by Univariate and Multivariate Classification Methods Downloads
Manuela Zucknick, Sylvia Richardson and Euan A. Stronach
Drifting Markov Models with Polynomial Drift and Applications to DNA Sequences Downloads
Nicolas Vergne
Accommodating Uncertainty in a Tree Set for Function Estimation Downloads
Brian C. Healy, Victor G. DeGruttola and Chengcheng Hu
Nonparametric Functional Mapping of Quantitative Trait Loci Underlying Programmed Cell Death Downloads
Yuehua Cui, Rongling Wu, George Casella and Jun Zhu
A Sparse PLS for Variable Selection when Integrating Omics Data Downloads
Kim-Anh Lê Cao, Debra Rossouw, Christèle Robert-Granié and Philippe Besse
Addressing the Shortcomings of Three Recent Bayesian Methods for Detecting Interspecific Recombination in DNA Sequence Alignments Downloads
Dirk Husmeier and Alexander V. Mantzaris
Supervised Distance Matrices Downloads
Katherine S. Pollard and Mark J. van der Laan
Importance Sampling for the Infinite Sites Model Downloads
Asger Hobolth, Marcy K. Uyenoyama and Carsten Wiuf
A Unification of Multivariate Methods for Meta-Analysis of Genetic Association Studies Downloads
Pantelis G. Bagos
Pattern Classification of Phylogeny Signals Downloads
Xiaofei Shi, Hong Gu and Chris Field
Quantifying the Association between Gene Expressions and DNA-Markers by Penalized Canonical Correlation Analysis Downloads
Sandra Waaijenborg, Philip C. Verselewel de Witt Hamer and Aeilko H. Zwinderman
Reducing Spatial Flaws in Oligonucleotide Arrays by Using Neighborhood Information Downloads
Jose Manuel Arteaga-Salas, Andrew P. Harrison and Graham J. G. Upton
Statistical Methods in Integrative Analysis for Gene Regulatory Modules Downloads
Lingmin Zeng, Jing Wu and Jun Xie
A Composite-Conditional-Likelihood Approach for Gene Mapping Based on Linkage Disequilibrium in Windows of Marker Loci Downloads
Fabrice Larribe and Sabin Lessard
Approximately Sufficient Statistics and Bayesian Computation Downloads
Paul Joyce and Paul Marjoram
Data Distribution of Short Oligonucleotide Expression Arrays and Its Application to the Construction of a Generalized Intellectual Framework Downloads
Tomokazu Konishi
Estimating Number of Clusters Based on a General Similarity Matrix with Application to Microarray Data Downloads
Shafagh Fallah, David Tritchler and Joseph Beyene
Collapsing SNP Genotypes in Case-Control Genome-Wide Association Studies Increases the Type I Error Rate and Power Downloads
Abigail G. Matthews, Chad Haynes, Chang Liu and Jurg Ott
A Comparison of Normalization Techniques for MicroRNA Microarray Data Downloads
Youlan Rao, Yoonkyung Lee, David Jarjoura, Amy S. Ruppert, Chang-gong Liu, Jason C. Hsu and John P. Hagan
Predicting Protein Concentrations with ELISA Microarray Assays, Monotonic Splines and Monte Carlo Simulation Downloads
Don Simone Daly, Kevin K. Anderson, Amanda M. White, Rachel M. Gonzalez, Susan M. Varnum and Richard C. Zangar
The Estimator of the Optimal Measure of Allelic Association: Mean, Variance and Probability Distribution When the Sample Size Tends to Infinity Downloads
Brigitte Mangin, Pauline Garnier-Géré and Christine Cierco-Ayrolles
Coalescent Time Distributions in Trees of Arbitrary Size Downloads
Sam Efromovich and Laura Salter Kubatko
Phenotyping Genetic Diseases Using an Extension of µ-Scores for Multivariate Data Downloads
José F. Morales, Tingting Song, Arleen D. Auerbach and Knut M. Wittkowski
Modeling DNA Methylation in a Population of Cancer Cells Downloads
Kimberly D. Siegmund, Paul Marjoram and Darryl Shibata
Detecting Two-Locus Gene-Gene Effects Using Monotonisation of the Penetrance Matrix Downloads
Susanne Henningsson and Staffan I. Nilsson
A SNP Streak Model for the Identification of Genetic Regions Identical-by-descent Downloads
Gregory Leibon, Daniel N. Rockmore and Martin R. Pollak
Semi-Parametric Differential Expression Analysis via Partial Mixture Estimation Downloads
David Rossell, Rudy Guerra and Clayton Scott
Re-Cracking the Nucleosome Positioning Code Downloads
Mark R. Segal
Adaptive Choice of the Number of Bootstrap Samples in Large Scale Multiple Testing Downloads
Wenge Guo and Shyamal Peddada
Adapting Prediction Error Estimates for Biased Complexity Selection in High-Dimensional Bootstrap Samples Downloads
Harald Binder and Martin Schumacher
TRAB: Testing Whether Mutation Frequencies Are Above an Unknown Background Downloads
Giovanni Parmigiani, Sining Chen and Victor E. Velculescu
Correcting the Estimated Level of Differential Expression for Gene Selection Bias: Application to a Microarray Study Downloads
David R. Bickel
Self-Organizing Maps with Statistical Phase Synchronization (SOMPS) for Analyzing Cell Cycle-Specific Gene Expression Data Downloads
Chang Sik Kim
Page updated 2009-11-25